Job ID = 2237036 sra ファイルのダウンロード中... Completed: 114156K bytes transferred in 5 seconds (172175K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 38010 0 38010 0 0 53391 0 --:--:-- --:--:-- --:--:-- 73236 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 5941311 spots for /home/okishinya/chipatlas/results/ce10/SRX080091/SRR298911.sra Written 5941311 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:33 5941311 reads; of these: 5941311 (100.00%) were unpaired; of these: 4731178 (79.63%) aligned 0 times 1009404 (16.99%) aligned exactly 1 time 200729 (3.38%) aligned >1 times 20.37% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 31030 / 1210133 = 0.0256 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Thu, 30 Apr 2015 11:25:24: # Command line: callpeak -t SRX080091.bam -f BAM -g ce -n SRX080091.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080091.20 # format = BAM # ChIP-seq file = ['SRX080091.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Thu, 30 Apr 2015 11:25:24: # Command line: callpeak -t SRX080091.bam -f BAM -g ce -n SRX080091.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080091.05 # format = BAM # ChIP-seq file = ['SRX080091.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Thu, 30 Apr 2015 11:25:24: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:24: # Command line: callpeak -t SRX080091.bam -f BAM -g ce -n SRX080091.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080091.10 # format = BAM # ChIP-seq file = ['SRX080091.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Thu, 30 Apr 2015 11:25:24: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:24: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:24: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:24: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:24: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:30: 1000000 INFO @ Thu, 30 Apr 2015 11:25:31: 1000000 INFO @ Thu, 30 Apr 2015 11:25:31: 1000000 INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:31: #1 total tags in treatment: 1179103 INFO @ Thu, 30 Apr 2015 11:25:31: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:31: #1 tags after filtering in treatment: 1179090 INFO @ Thu, 30 Apr 2015 11:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:31: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:31: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:32: #2 number of paired peaks: 306 WARNING @ Thu, 30 Apr 2015 11:25:32: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:32: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:32: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:32: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:32: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:32: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:32: #1 total tags in treatment: 1179103 INFO @ Thu, 30 Apr 2015 11:25:32: #1 total tags in treatment: 1179103 INFO @ Thu, 30 Apr 2015 11:25:32: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:32: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:32: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:32: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:32: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:32: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:25:32: #2 alternative fragment length(s) may be 32,120,217,445,479,502,574 bps INFO @ Thu, 30 Apr 2015 11:25:32: #2.2 Generate R script for model : SRX080091.10_model.r WARNING @ Thu, 30 Apr 2015 11:25:32: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:32: #2 You may need to consider one of the other alternative d(s): 32,120,217,445,479,502,574 WARNING @ Thu, 30 Apr 2015 11:25:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:32: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:32: #1 tags after filtering in treatment: 1179090 INFO @ Thu, 30 Apr 2015 11:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:32: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:32: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:32: #1 tags after filtering in treatment: 1179090 INFO @ Thu, 30 Apr 2015 11:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:32: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:32: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:33: #2 number of paired peaks: 306 WARNING @ Thu, 30 Apr 2015 11:25:33: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:33: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:33: #2 number of paired peaks: 306 WARNING @ Thu, 30 Apr 2015 11:25:33: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:33: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:33: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:33: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:33: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:33: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:25:33: #2 alternative fragment length(s) may be 32,120,217,445,479,502,574 bps INFO @ Thu, 30 Apr 2015 11:25:33: #2.2 Generate R script for model : SRX080091.05_model.r WARNING @ Thu, 30 Apr 2015 11:25:33: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:33: #2 You may need to consider one of the other alternative d(s): 32,120,217,445,479,502,574 WARNING @ Thu, 30 Apr 2015 11:25:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:33: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:33: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:33: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:33: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:33: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:25:33: #2 alternative fragment length(s) may be 32,120,217,445,479,502,574 bps INFO @ Thu, 30 Apr 2015 11:25:33: #2.2 Generate R script for model : SRX080091.20_model.r WARNING @ Thu, 30 Apr 2015 11:25:33: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:33: #2 You may need to consider one of the other alternative d(s): 32,120,217,445,479,502,574 WARNING @ Thu, 30 Apr 2015 11:25:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:33: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:39: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:40: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:41: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:44: #4 Write output xls file... SRX080091.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:44: #4 Write peak in narrowPeak format file... SRX080091.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:44: #4 Write summits bed file... SRX080091.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:45: #4 Write output xls file... SRX080091.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:45: #4 Write peak in narrowPeak format file... SRX080091.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:45: #4 Write summits bed file... SRX080091.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:45: #4 Write output xls file... SRX080091.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:45: #4 Write peak in narrowPeak format file... SRX080091.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:45: #4 Write summits bed file... SRX080091.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。